Re: [bug #17329] Diffusion Tensor PDB creation is broken -- January 11, 2011 - 10:01

Hi,

Would you have a PDB file and a mini-script with truncated data (or
set of instructions for the GUI) to be able to reproduce this bug?
This looks like the internal PDB reader has been used on a PDB file
with the element column missing, and that the internal reader cannot
determine the element type of one of the important atoms.

Cheers,

Edward



On 16 December 2010 04:59, Michael Bieri
<NO-REPLY.INVALID-ADDRESS@xxxxxxx> wrote:
> URL:
>  <http://gna.org/bugs/?17329>
>
>                 Summary: Diffusion Tensor PDB creation is broken
>                 Project: relax
>            Submitted by: michaelbieri
>            Submitted on: Do 16 Dez 2010 14:59:48 EST
>                Category: None
>                Severity: 3 - Normal
>                Priority: 5 - Normal
>                  Status: None
>                 Privacy: Public
>             Assigned to: michaelbieri
>         Originator Name:
>        Originator Email:
>             Open/Closed: Open
>         Discussion Lock: Any
>                 Release: Repository: 1.3 line
>        Operating System: None
>
>    _______________________________________________________
>
> Details:
>
> By trying to create a diffusion tensor pdb representation (either after
> running the GUI or the diff_tensor_pdb.py script) the following error 
> occurs:
>
> Traceback (most recent call last):
>  File "/usr/local/bin/relax", line 390, in <module>
>    Relax()
>  File "/usr/local/bin/relax", line 123, in __init__
>    self.interpreter.run(self.script_file)
>  File "/home/michael/Programme/relaxGUI/prompt/interpreter.py", line 290, in
> run
>    return run_script(intro=self.__intro_string, local=locals(),
> script_file=script_file, quit=self.__quit_flag,
> show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
>  File "/home/michael/Programme/relaxGUI/prompt/interpreter.py", line 536, in
> run_script
>    return console.interact(intro, local, script_file, quit,
> show_script=show_script, raise_relax_error=raise_relax_error)
>  File "/home/michael/Programme/relaxGUI/prompt/interpreter.py", line 432, in
> interact_script
>    execfile(script_file, local)
>  File "diff_tensor_pdb.py", line 15, in <module>
>    structure.create_diff_tensor_pdb(file=tensor_file, force=True)
>  File "/home/michael/Programme/relaxGUI/prompt/structure.py", line 148, in
> create_diff_tensor_pdb
>    generic_fns.structure.geometric.create_diff_tensor_pdb(scale=scale,
> file=file, dir=dir, force=force)
>  File "/home/michael/Programme/relaxGUI/generic_fns/structure/geometric.py",
> line 471, in create_diff_tensor_pdb
>    CoM = centre_of_mass()
>  File "/home/michael/Programme/relaxGUI/generic_fns/structure/mass.py", line
> 95, in centre_of_mass
>    mass = return_atomic_mass(element)
>  File "/home/michael/Programme/relaxGUI/physical_constants.py", line 257, in
> return_atomic_mass
>    if upper(element) == 'CA':
>  File "/usr/lib/python2.6/string.py", line 235, in upper
>    return s.upper()
> AttributeError: 'NoneType' object has no attribute 'upper'
>
>
>
>
>
>    _______________________________________________________
>
> Reply to this item at:
>
>  <http://gna.org/bugs/?17329>
>
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